You are justified in having misgivings about the info in the death certs. Misheard/misunderstood or poor spelling.
The cert you have for Hannah/Anna is the correct one despite children not being recorded. The info on Hannah/Anna was advised by dtr Susan who seems to have been the go-to person in a number of instances (sister Elizabeth's inquest). The spelling of Clark/e is uncertain - the marriage record in Cape Town has the name Clarke, birthplace Warwickshire, England. No ages, parents etc. Their marriage was also noted in a Cape Town newspaper, but only initials whereas most others had full first names.
Like you and despite some Warwickshire records being accessible online, unable to find anything relating to Thos' wife Susan, or Hannah's birth. The use of the names Thomas and Susan for Robt Jos and Hannah's older children tends to suggest strong possibility of them being Hannah's parents names. Just finding them is the problem. Thos noted as a farmer may help although they may have come from a neighbouring county.
This doesn't get us any closer to an answer, but little bits here and there may eventually get us over that wall.
Garry